Purpose: Although many studies have analyzed the suitability of different grafting materials for maxillary sinus augmentation by means of histomorphometry in conventional histologic strains, the three-dimensional (3D) structure and remodeling of these grafts after healing beneath the sinus membrane remain unclear. The aim of the present study was to determine whether microcomputed tomography is a suitable method to evaluate the 3D structure and remodeling of grafts after sinus floor augmentation. Materials and Methods: Sinus floor augmentation was performed in five patients using autogenous bone (AB) alone, AB and beta-tricalcium phosphate (b-TCP, Cerasorb), AB and b TCP/hydroxyapatite (HA) (BoneCeramic), AB and calcium carbonate (Algipore), and AB and HA (PepGen). Specimens from the grafted sites were harvested by means of a trephine bur 5 to 16 months after maxillary sinus augmentation. Microcomputed tomography of these specimens was performed with a nominal isotropic resolution of 6 3 6 3 6 µm2 voxel size. After segmentation, 3D images were reconstructed, and the distribution of bone and substitute material was evaluated by means of volumetric and density measurements. Results: In all images, both bone and substitute material could clearly be identified. The connectivity of trabeculae surrounding the substitute material was visible in the 3D reconstructions. Volumetric evaluation such as total bone volume, volume of substitute material, and trabecular thickness and spacing revealed differences between the different grafting materials. Conclusion: Microcomputed tomography is a promising method to evaluate the 3D structure of grafts after sinus floor augmentation with autogenous bone and bone substitute materials. Keywords: bone grafting, maxillary sinus augmentation, microcomputed tomography